ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Abstract

The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org.

Keywords: NCBI taxonomy; hypothesis testing; phylogenetics.; phylogenomics; tree comparison; tree visualization.

Fig. 1

Several phylogenetic tree images generated using the ETE toolkit. (A) Gene tree reconstructed using ete-build. The figure shows the relationships between several P53 genes together with their aligned sequences visualized in condensed format. (B) Tree image generated by ete-evol for three models fitted to a classical example (Bielawski and Yang 2004). (i) The line chart on top of the alignment indicates the omega estimates for sites as calculated by the SLR software. (ii) The bar chart at the bottom part shows the dn/ds ratio for each site under the M2 site-model from CodeML. Line colors in both charts indicate the significance of assigning a site to a given class of positive selection (i.e., red for P-value <0.01 and orange for P-value <0.05). (iii) The color and size of tree nodes represent the dn/ds ratio estimated for tree branches using the free-ratio model from CodeML. Blue small circles indicate a ratio between 0.2 and 1, medium yellow nodes indicate a ratio >1, and big red nodes for infinite values. Note that the right side panel allows users to select the models to be displayed, and even starting new runs using predefined models. (C) Portion of a recently published bird species tree (Jarvis et al. 2014) annotated with gene–tree support values (blue spheres), custom node labeling (first aligned column) and taxonomic information (next aligned columns). (D) Example of a phylogenetic tree visualized with a sequence alignment and domain composition as used in the eggNOG database (Huerta-Cepas et al. 2016).